In January 2007 it was reported that Klasnić suffered kidney failure, Klasnić shortly after received a kidney transplantation, but not long afterwards, his body rejected the kidney his mother Šima donated. On March 23, 2007 he underwent surgery to replace the rejected kidney. This time receiving a kidney from his father. Klasnić released the following statement: "Thank God, the transplant went very well. My body accepted my father's kidney and we're both doing well. The doctors already told me I would be able to continue playing football."
However in August 2007 the doctors at Werder Bremen forbade him to train due to inability of his body to whitstand heavy physical strain.
In September 2007 doctors finally allowed Ivan Klasnić to attend full training after he was absent for about 6 months. He then joined the team and made a couple appearances in the club's cup activities and also appeared in a few matches for the second team. However, on November 24, 2007 Ivan was selected to start for Werder for the first time since December 2006, and played 65 minutes for his team in a Bundesliga match against Energie Cottbus. Klasnic completed his comeback on December 15, 2007, scoring twice in Bremen's 5-2 victory over Bayer Leverkusen, playing 85 minutes. In March, 2008, Ivan was recalled to national team after a year absence.
