A cross-sectional study was carried out in 200 children aged 5–15 years, to examine the presence of intestinal parasitic infections (IPIs) and to assess the risk factors and clinical features associated with them in children in San Juan y Martinez (SJM), Cuba. Three fresh faecal samples were collected from each child and were examined by direct wet mount, brine flotation, formalin-ether and Kato-Katz techniques. Data relating to demography, source of drinking water, personal hygiene habits and clinical features were also collected. Living in the rural area was significantly associated with the highest infection rates (p < 0.01). According to clinical features and laboratory examinations, children with abdominal pain were about four times more likely to have IPIs (OR 4.05, CI, 1.11, 13.18) especially soil-transmitted helminths (STH). We suggest that IPIs, especially STH, in SJM should be strongly suspected in children with abdominal pain from rural areas. Targeted and frequent interventions to control these infections are needed in this municipality.