Liver resection is a widely preferred treatment modality for hepatocellular carcinomas (HCCs). This study aimed to compare the survival impact of anatomical resection with that of limited resection, in patients with single HCCs no larger than 5 cm in diameter. A cohort study was carried out on 209 consecutive patients who underwent hepatic resection for a single HCC no larger than 5 cm in diameter between January 1994 and March 2007 at Osaka City General Hospital. The cumulative 5-year overall survival and disease-free survival rates in the anatomical resection group (n = 111) were 71 and 40%, respectively, both of which were significantly better than the 48 and 25% seen in the limited resection group (n = 98) (P = 0.0043 and P = 0.0232, respectively). Better effects of the anatomical resection on both overall and disease-free survival were seen in patients having HCC larger than 2 cm in diameter and in patients with moderately or poorly differentiated HCC. But no significant difference in either overall or disease-free survival was seen between the groups in patients with a HCC 2 cm or less in diameter or in the patients with well-differentiated HCC. Using Cox's regression model, anatomical resection was confirmed to be an independent favorable factor for both overall and disease-free survival. Anatomical resection is therefore recommended for histologically advanced single HCCs ranging from 2 to 5 cm in diameter.