The present study examined the possibility of using a tissue subsample to estimate the total number of Schistosoma japonicum eggs in the liver or an intestinal section. Sixteen male Landrace/Yorkshire crossbred pigs were each infected with 500 S. japonicum cercariae and killed 12 weeks post infection. Five-gram samples were taken from specific areas of the liver, colon, caecum and rectum, and tissue egg counts (TECs) were determined by digestion of the tissue sample in 3% KOH for 18 h according to a standard procedure. The rest of each tissue was also processed to determine whole tissue egg counts. For the liver, counts from 5-g samples taken from the left medial and left lateral lobes were not significantly different from counts for the whole liver, but counts from 5-g samples from the right lateral, right medial and central lobes differed significantly from whole liver counts. Variable results were obtained for 5-g samples from six specific points in the colon in comparison with the whole colon counts. This latter result corresponded well to observed gross pathological findings indicating patchy egg deposition in the large intestine. One 5 g sample from either the caecum or rectum could not be used to estimate the whole tissue egg count because of the high variability in the counts. The results suggest that the processing time of liver tissue can be greatly diminished by using a 5 g subsample from a specific liver lobe to estimate the TEC of the whole organ.