This study investigated the prevalence, risk factors and species composition of ticks, fleas and lice infesting dogs and cats in and around Hawassa in southern Ethiopia. In total, 200 dogs and 100 cats were examined from November 2008 to April 2009. Of the dogs and cats examined, 99.5% and 91.5%, respectively, were infested with one or more species of ticks, fleas or lice. The overall prevalence was higher in dogs than in cats. A total of six different species of ectoparasites were collected and identified from dogs, but only three species from cats. Ctenocephalides felis was the predominant species amongst the animals, with a prevalence of 82.9% on dogs and 67% on cats. Other prevalent species on dogs included Ctenocephalides canis (73.8%), Heterodoxus spiniger (4%), nymphs of Amblyomma spp. (3.5%), Pulex irritans (2.5%) and Haemaphysalis leachi (0.5%). C. canis (18%) and P. irritans (6%) were also found on cats. More female than male fleas and lice were observed. The study revealed that the prevalence of fleas, ticks and lice on dogs was not significantly different between male and female animals or between young and adult dogs. However, the prevalence of these ectoparasites was significantly higher in female than in male and in adult than in young cats. The study showed that the prevalence of ectoparasites on both dogs and cats was significantly higher on animals with flea allergy dermatitis (FAD) than those without FAD, and on animals with lesions on their skin compared with those without lesions.