Aims: The aim of the study was to investigate the flock prevalence of Campylobacter jejuni and Campylobacter coli in broiler farms in Lithuania and to identify possible persistent strains of Camp. jejuni using amplified fragment length polymorphism (AFLP) typing method. Methods and Results: During 1 year, 42 broiler flocks from 9 broiler farms were examined to determine the prevalence of Campylobacter-positive broiler flocks in Lithuania. Among 42 broiler flocks examined, 31 flocks (73 center dot 8%) were positive for Camp. jejuni and 17 flocks (40 center dot 48%) for Camp. coli. Campylobacter jejuni isolates were genotyped by AFLP method using BspDI and BglII restriction enzymes. Typing of 190 isolates generated 50 AFLP genotypes with the highest diversity of strains found in the summer season. Each farm showed one or more predominant AFLP types, and one AFLP type (A32) was found in five broiler farms over a 1-year period. Conclusions: Campylobacter jejuni and Camp. coli are highly prevalent in broiler farms in Lithuania. Farm-specific genotypes were identified in all farms examined. Type A32 was present and persisted in different broiler farms, and a common source of transmission of Camp. jejuni was suspected. Significance and Impact of the Study: For the first time, Camp. jejuni in broiler flocks has been genetically characterized in Lithuania. Persistent strains of Camp. jejuni were detected over one period at the beginning of broiler meat production chain and, therefore, the identification of contamination source of such strains and the mechanism of their particular ability to persist are crucial to establish effective control measures against Camp. jejuni infection in broiler farms.