Although intestinal parasitic infections (IPI) among children remain a global issue, the current information on such infections in Albanian children is very limited. A cross-sectional study of the IPI in 321 children living in the Albanian counties of Tirana (152) and Elbasan (169) was therefore conducted in 2008, with a pre-tested standard questionnaire employed to gather the relevant personal and clinical data. Using formalin-ether concentration and permanent stains, stool samples were examined microscopically for the ova, cysts and oocysts of any parasites. The overall prevalence of IPI was 19% (61 of 321), with protozoan infections (11·5%) apparently more common than infections with soil-transmitted helminths (STH; 8·1%). Giardia duodenalis was the parasite most frequently detected (10·9%), followed by hookworm (5·6%), Ascaris lumbricoides (1·9%), Trichuris trichiura (0·6%), Cryptosporidium (0·3%) and Entamoeba histolytica/dispar (0·3%). The results of a univariate analysis indicated that the children from Tirana county were significantly more likely to be found infected with STH compared with the children from Elbasan county (12·5% v. 4·1%; P=0·006). Children sampled in the community were also more likely to be found STH-positive than the children sampled as they attended hospitals and health clinics (10·5% v. 6·0%) but this difference did not reach statistical significance. The children found STH-positive were five times more likely to be suffering from diarrhoea than the other children checked in clinical settings (P=0·004) and were also more likely to be suffering from abdominal pain (P=0·054) and/or diminished appetite (P=0·016).