The significance of dissecting the lateral pelvic lymph node (LN) for lower rectal cancer remains controversial. We detected the lateral sentinel node (SN) by indocyanine green (ICG) and micrometastases using carcinoembryonic antigen (CEA)-specific reverse transcriptase-polymerase chain reaction (RT-PCR). Twenty-five patients who underwent curative surgery with a dissection of the lateral pelvic LNs between 2003 and 2005 were examined. We investigated the existence of lateral SNs and any associations between pathological metastases and micrometastases by RT-PCR. Lateral SNs were detected in 7 (28%) of the 25 patients. The number of lateral SNs was 13 LNs, or 1.9 nodes per case. Of the 25 cases, 7 had lateral LN metastases based on pathological examinations in dissected lateral LNs. Three cases had massive lateral LN swelling by pre-operative pelvic CT and the SNs were not detected in them. The SNs were detected in two cases and were negative based on pathological examinations and positive according to a genetic diagnosis. SNs were detected in one case, which was positive based on pathological examinations and a genetic diagnosis. SN was not detected in one case. There were five SNs in which CEA was positive by RT-PCR, though only one of them was positive based on pathological examinations. No SNs were observed that were negative based on a genetic diagnosis, but were positive according to the pathological diagnosis. We detected the lateral SNs using ICG. The sensitivity of identifying lateral LN metastasis was improved by the use of a genetic diagnosis. However, the detection rate was still low, therefore we need to develop a new method for detecting SNs.