The two procedures use entirely different estimation methods. Conditional logistic regression in PROC LOGISTIC maximizes a conditional likelihood, while PROC GENMOD uses the Generalized Estimating Equations (GEE) method which is not a likelihood-based method. These methods, and others, are compared in the book "Logistic Regression Using SAS: Theory and Application, Second Edition," (Allison, P., SAS Institute, 2012).
... View more