Giardiosis and cryptosporidiosis are frequently diagnosed in calves at the large animal clinic of the veterinary school. Few studies have been reported in the literature regarding pathogenesis of these two intestinal protozoa. The aims of this study were to follow the histological changes in the villi and crypts and the changes in the number of intraepithelial lymphocytes in the jejunum of naturally infected calves during the acute phase of infection. For this purpose, 29 calves aged between 7 and 10 days were bought at a local auction. The animals were housed in individual pens to avoid cross-contamination. Fecal samples were examined microscopically for the presence of Giardia cysts and Cryptosporidium oocysts, three times per week for a period of 45 days. Six calves did not pass any cysts or oocysts and were used as controls. Fifteen calves passed Giardia cysts only, five passed both cysts and oocysts, and three passed oocysts only. The villus to crypt ratio index was 1.76 in the control group and 1.08 in the Giardia-infected group. In the Cryptosporidium-infected calves, the ratio was 1.18 and calves infected with both parasites had an index of 1.37. The number of intraepithelial lymphocytes per millimeter of jejunum tissue was 21 in the control group. This number was doubled in the calves infected with Giardia, but was slightly lower in the other infected groups. All of the infected calves had intermittent diarrhea and mucus was seen in many fecal samples.