The aim of this study was to investigate relationship between Faecal Egg Counts (FECs) and protein excretion in naturally acquired nematode infected Moghani ewes. Thirty-five Moghani ewes (aged from 6 to 12 months and average of body weight 32±3 kg) were selected among the naturally acquired nematode infected animals which their infection had confirmed by McMaster flotation method. The animals were divided into 5 groups according to the FECs (<320, 320-370, 370-420, 420-470 and >470). Faecal samples were taken directly from the rectum of each animal in early morning and kept in individual sampling containers under 4℃. Faecal parameters such as Crude Protein (CP), Dry Matter (DM), Organic Matter (OM) and ash were determined using the Kjeldahl method following the standard procedures. Data were processed in excel and statistical analysis was performed using SPSS/ver. 17 software. Our data indicates that there was a significant difference among groups for the faecal ash and OM values (p<0.05) in the studied animals. Also, we observed a significant correlation between the ash and OM values (p<0.001, r=-0.952). In addition, there was a negative but not significant correlation between the FECs and CP values (p>0.1, r=-0.290) in the naturally acquired nematode infected Moghani ewes. In conclusion, the FECs was not a good indication for interpretation of faecal protein excretion in nematode infected sheep.