Human immunodeficiency virus (HIV)-infected children generally show poor growth. Episodes of diarrhoea and pneumonia in HIV-infected children are thought to be more severe than in HIV-uninfected children. The objective of this study was to compare duration of hospitalization, appetite and nutritional status of HIV-infected children with that of uninfected children. A cross-sectional study was performed on children (2–24 months) admitted with diarrhoea or pneumonia to the university hospital. Children were tested for HIV, and the duration of hospitalization was noted for 189 children. Follow-up for blood analysis (n = 154) and appetite measurement (n = 48) was performed 4–8 weeks after discharge. Appetite was measured as ad libitum intake of a commercial infant cereal using highly standardized procedures. Hospitalization (in days) was significantly longer in HIV-infected children; among children admitted with diarrhoea (5.9 ± 1.9 vs. 3.8 ± 1.5) (mean ± standard deviation) and with pneumonia (9.0 ± 2.5 vs. 5.9 ± 1.9). Serum zinc, iron and transferrin concentrations, and haemoglobin levels were significantly lower in HIV-infected children compared with uninfected children. Appetites [amounts eaten (g) per kg body weight] of HIV-infected children were significantly poorer than those of HIV-uninfected children (18.6 ± 5.8 vs. 25.2 ± 7.4). The eating rates (g min−1) of HIV-infected children were also slower (17.6 ± 6.2 vs. 10.1 ± 3.7) Mean Z-scores for length-for-age were significantly lower among HIV-infected children compared with HIV-uninfected children. Weight-for-length Z-scores were not significantly different. In summary, HIV-infected children had a 55% longer duration of hospitalization and a 21% lower appetite.