Recovery of bacteria from shell eggs is important for evaluating the efficacy of processing and the quality and safety of the final product. Shell rinse (SR) techniques are easy to perform and widely used. An alternative sampling method involves crushing and rubbing the shell (CR). To determine the most appropriate method for recovering microorganisms from shell eggs, 358 shell eggs were collected from a commercial egg processor and sampled by SR and CR techniques. Total aerobic mesophiles and Enterobacteriaceae were enumerated on plate count and violet red bile glucose agar plates, respectively. Unwashed, in process, and postprocess eggs were evaluated in the study. Aerobic microorganism prevalence for eggshells sampled was similar for both methods (approximately 100%), but the log CFU per milliliter values were higher in the SR than the CR samples (3.2 and 2.2, respectively). Average Enterobacteriaceae recovery was similar for both methods (45 versus 40% for the SR and CR methods, respectively) when all eggs were considered together. This population was detected more often by SR when unwashed eggs were sampled (90 versus 56% for the SR and CR methods, respectively), equally by SR and CR for in-process eggs (30 versus 29.3% for the SR and CR methods, respectively), but more often by CR for postprocess eggs (10 versus 36% for the SR and CR methods, respectively). The SR technique was easier to perform and recovered larger numbers of aerobic organisms, particularly for unwashed eggs. However, the CR technique was more efficient for recovery of Enterobacteriaceae from postprocess eggs. Stage of shell egg processing may be an important consideration when choosing egg sampling methods.