In 1989–2000 archeological investigations in the courtyard of the castle revealed a level of cultural layers that formed after the destruction of the first castle in 1362 up to the construction of the second - the stone - castle. This period should be ascribed to the third stage of the site of Kaunas castle, during which wooden-clay fortifications were built (pic. 1). The fortifications were situated within the perimeter of the southern walls that surrounded the courtyard of the castle destroyed in 1362. After the destruction of the first castle, within the limits of the former wall perimeter the debris mound formed covering the remains of the walls. These mounds were later used in the construction of the woodenclay fortifications (Pic. 2). Most probably, the mould was used as a base for wooden fortification walls covered with clay. The discovered remains of the fortifications show that there used to be three parallel fosses dug in the north-south direction with a row of stakes between the second and the third fosse (Pic. 2). In the southwest corner of the castle site a rectangular wooden building was constructed measuring 9.5–10 meters in width. Its walls could have been constructed of vertically positioned balks covered with a thick layer of clay. If the building performed any defensive functions, it most probably also had the second story. The building was positioned in the north-south direction and stood ca. 5 meters to the south of edge of the slope descending to the Neris river. The length of the building is impossible to determine, since the Neris most probably washed its northern end away, and the remains of the southern end were destroyed during the construction of the southwest tower of the stone castle. The building was divided into two main internal chambers: the western room was ca. 3.6 meters wide, and the eastern one – ca. 5.3 meters wide. There also could have been a wooden defensive wall standing on the western debris mound between the western wall of the building and the slope of the Neris river. […]

The first Kaunas castle was one of the four castellum-type castles built on the territory of the Grand Duchy of Lithuania in the middle of the XIVth century. It was situated on the left coast of the Neris, approximately 6,00 metres to the north-east from the confluence of the Nemunas and the Neris, in a neglected archaic settlement (pic.l). According to the findings, the settlement dates back to the Xth - XIIth century (pic. 2). By the end of the XIXth century the Neris had washed away the main part of the castle (pic. 3). The defensive complex of the castle, the size of about 4 hectares, consisted of a trapezium stone castle with the walls of 12 metres high and 2.5 metres thick, the defensive ditches in the eastern and southern parts, defensive fortifications at the bottom of the defensive ditch and two brick towers (pics. 3, 11-13). The walls of the castle were made of stone (pics. 4-5), whereas the shooting gallery, gates and most probably the top of the walls and the decoration band on the external walls were made of brick. The area of the castle yard was 5200 m2. The investigation shows that the construction of all planned fortifications had not been finished until the attack on the castle in 1362 (pic. 10). It is estimated that for the building of the castle about 16,000 m3 of building materials was utilised. From the defensive ditch about 70,000 m3 of gravel must have been dug out. In the yard of the castle there were wooden houses and outbuildings (pic. 6). During the period of research very few artifacts were found, and these include pots decorated with stamped ornaments (pics. 7, 8). The main body of findings consists of a crossbow, an arch and balista arrow-heads lost during the attack in 1362 (pic. 9). The real possibilities and conditions for building the first Kaunas castle were already existant at the end of Gediminas' rule. However, the necessity of doing this in practice arose after the Strėva battle in 1348 due to the fact that the march of the Order of Crusaders was the first real menace to Vilnius, the capital of the Great Duchy of Lithuania. The spade work of building the first Kaunas castle started in 1359-1360, the construction was started in 1361 but it had not been finished until the spring of 1362.

The war between the Lithuanians and the Teutonic Order in Prussia began in 1283. Until the middle of the 14th century, the Order would attack the western part of Lithuania. With the destruction of the Kaunas stone castle in spring 1362, the Order began to organize intensive attacks of the heart of the Lithuanian state and marches to Trakai and Vilnius. The Livonian Order was devastating the northern Lithuania. The function of the first Kaunas castle, built in 1361-1362, was to protect the state from the west and secure the waterway to Vilnius by the river Neris. Kaunas castle was the first of the four fence-type stone castles built in the Grand Duchy of Lithuania in the 14th century (Medininkai, Lyda and Krėva castles were built in 1370-1380). The smallest in size, the Kaunas castle was the last to be taken by the army of the Teutonic Order. Finally, it was demolished and never rebuilt. The siege and assault of the castle occurred on March 29th-April 17th, 1362. The crusaders from Prussia were joined by guest knights from England, Italy, Germany and the army of the Livonian Order. 350 Lithuanian fighters died, whereas 36 survivors and the duke Vaidotas were taken captive. The crusaders demolished the castle and burned the eastern settlements. After the destruction of the Kaunas castle, the surroundings at the confluences of the Nemunas, Neris and Nevėžis became the war front. The fights between the Lithuanians and the Order lasted until the beginning of the 15th century. In 1363-1369, the castles of New Kaunas and Gotteswerder on the island of Virgalė were constantly fought for. The crusaders destroyed the castles of Pieštvė and Veliuona in 1363, the Paštuva castle in 1370, and the Eiguliai castle in 1382. In 1384, the Lithuanians destroyed Marienwerder, the most powerful castle of crusaders in Lithuania built at the confluence of the Nemunas and the Neris, whereas in 1392 – a wooden castle of Ritersveder near Kaunas. Only around 1396, the first wooden and earthen defensive constructions were built on the ruins of the first Kaunas castle (burnt by Lithuanians in 1401). In 1402, the Lithuanians burnt the Gotteswerder castle. The last record of crusader attack in Kaunas was in 1403. In 1404, Lithuania and the Order signed a peace treaty of Raciąż. During the period of peace in 1404-1409 (until the uprising of Samogitians against the Order), in the place of the first castle, the second castle of Kaunas was built, the remains of which have survived to the present days. The new castle with a crew of 600 people is mentioned in the letter of the Komtur of Ragainė for the Grand Master of the Order, in November, 1409. The existing interpretations that Kaunas castle was rebuilt in 1363, 1368 or 1369 are false as these dates are related to the castles of the New Kaunas or Gotteswerder, situated on the island of Virgalė. Also, the stereotypical claim that Kaunas castle was constantly attacked by crusaders is also ungrounded as it is evident that the castle was attacked and destroyed only in the spring of 1362, whereas the second castle was never attacked.

After the destruction of the Kaunas castle in 1362, one of the objects of fights between the Lithuanians and the Teutonic Order in the sixth decade of the 14th century became the castle of New Kaunas built by Lithuanians and the Gotteswerder castle built by the Teutonic Order, both situated in the same place at the confluence of the Nemunas and the Nevėžis. The exact place of these castles is not known apart from the fact that they were on an island. The archival sources of the end of the 14th century do not mention the placename of New Kaunas. The sources of the 15th-17th centuries mention Gotzwerd instead of Gotteswerder as an island of the Nemunas situated against the fields of Wedesa. The fields extended between the Nemunas, its arm the Niemnina and the Nevėžis. On the other hand, Gotzwerd is not indicated in the extant plans of the 18th century. The satellite image of the confluence of the Nemunas and the Nevėžis does not show any evidence of such island in the Nemunas. Summarizing, it can be said that the island of Nemunas called Gotzwerd was submerged in the 18th century. Therefore, an archaeological investigation of Wedesa fields between the Nemunas and the presently extinct Niemnina is necessary. As it has been mentioned, the castles of Gotteswerder and New Kaunas were complex defence constructions, which could hardly be situated on a small island in the middle of the river.