Hnilicka's contract was up again and decided that joining one of the league's weaker clubs would give him a better chance of becoming an NHL regular.

Hnilicka signed with the Atlanta Thrashers that summer, and though the team lacked depth, he was still considered a long shot to make the club. However, after a solid training camp he gave the team's brass little choice but to keep him and re-assign fellow netminder Norm Maracle. Hnilicka and veteran goaltender Damian Rhodes shared the duties for Atlanta, and though he played two less games then his partner, he led the club in wins with 12. The following year Rhodes' season was all but a write off due to chronic injuries and Hnilicka became the club's undisputed starting goalie, and he madethe most of the opportunity. In sixty games he posted an impressive .908 save percentage and had a respectable 3.19 goals against average as well.

When the Thrashers failed to qualify for the Stanley Cup Playoffs Hnilicka was invited to participate in the World Championships for the Czech Republic. He played fantastic through the first four games of the tournament before falling to Russia in the Quarterfinals.

Hnilicka went to split his 2002-03 season between the Thrashers and the team's AHL affiliate in Chicago before being acquired by the Los Angeles Kings prior to the 2003-04 NHL season.

Signed as a free agent by NY Rangers, July 15, 1999. Signed as a free agent by Atlanta, July 28, 2000. Traded to Los Angeles by Atlanta for future considerations, September 15, 2003.