Guidelines from two major organizations have recently supported the use of only the serological marker carcinoembryonic antigen (CEA) for the prognostication and monitoring of patients with colorectal carcinoma. However, in view of the exciting advances made recently in elucidating the molecular and cellular biology of adenocarcinoma of the rectum, the molecules that transform the well-ordered normal rectal epithelium into an invasive adenocarcinoma may yield information about the ultimate behavior of that cancer. Consequently, assessing the expression of molecules within a primary cancer may predict the probability of regional and distant metastasis, response to therapy, and outcome. This review analyzes the current state of intratumoral expression of several molecular markers for the management of rectal cancer and evaluates their potential for defining which patients may undergo rectal sphincter preservation and need adjuvant therapy.