Submitting tissue samples via mail may present challenges to practitioners with respect to public health, public perception, and regulatory restrictions. Considering these challenges of tissue sampling, the objective of this pilot study was to evaluate alternative sampling techniques for the detection and characterization of Escherichia coli (E. coli) in field cases of diarrhea in weaned pigs. Rectal swabs offer a practical alternative to tissue sampling because they potentially decrease the need for tissue sampling and allow an increased sample size in a more cost effective manner. Rectal swab samples were compared to intestinal tissue samples from the same pig to compare the frequency of E. coli isolation, and agreement of both antibiograms and genotyping for pilus and toxin genes. Diagnostic results were evaluated for agreement at the pig and farm level. E. coli was isolated from all cases using both rectal swabs and intestinal tissue. The genotyping results from the rectal swab and the intestinal tissue did not agree at the pig level in 64% of the cases. This suggests that multiple samples are required to characterize the E. coli population in field cases, and if both results are considered, we are more likely to choose an effective treatment to cover the entire population. Rectal swabs and tissue samples both have individual advantages and disadvantages to the practitioner. Tissue samples give the practitioner the ability to necropsy the pig and therefore view systematic lesions and other pathogens. Rectal swabbing may provide an opportunity for practitioners to submit a greater number of samples per farm to better characterize the E. coli population without euthanizing additional pigs but may not replace tissue derived diagnostics entirely. When facing a difficult E. coli challenge or poorly represented and identified populations, we can cost effectively increase the sample size by adding rectal swabbing to current diagnostic tools.