Pneumocystis pneumonia was identified in two female (cases 1 and 2) and a male (case 3) Boer cross goat kids aged 3 months on a farm in Uganda. This was fatal in cases 1 and 2, with symptoms of coughing. Severe infestation with Haemonchus contortus was found in the euthanized case 3. Histology revealed numerous Pneumocystis organisms in cases 1 and 2, but fewer in case 3. Although macrophages reactive to the organisms were observed in all cases, the lung lesions were not infiltrated with lymphocytes in cases 1 and 2. Polymerase chain reaction analysis for Pneumocystis DNA identified five genetic clones in case 1. This diversity may be due to repeated infection from other goats, and may also be associated with selective pressure from the innate immune system activated by mild Haemonchus infestation in young kids.