The presence of Rickettsia felis, Bartonella henselae and B. clarridgeiae in 209 fleas (Ctenocephalides felis) obtained from domestic cats and dogs in several locations in Malaysia was investigated in this study. Using a polymerase chain reaction specific for the citrate synthase (gltA) and 17-kD antigenic protein (17kD) genes of rickettsiae, we detected R. felis DNA in 6 (2.9%) fleas. For detection of bartonellae, amplification of the heme-binding protein (pap31) and riboflavin synthase (ribC) genes identified B. henselae and B. clarridgeiae DNA in 24 (11.5%) and 40 (19.1%) fleas, respectively. The DNA of B. henselae and B. clarridgeiae was detected in 10 (4.8%) fleas. Two B. henselae genogroups (Marseille and Houston-1) were detected in this study; genogroup Marseille (genotype Fizz) was found more often in the fleas. The findings in this study suggest fleas as potential vectors of rickettsioses and cat-scratch disease in this country.