Microbiological analyses of fruits and vegetables produced by farms in Minnesota and Wisconsin were conducted to determine the prevalence of Escherichia coli in pre-harvest fruits and vegetables. During the 2003 and 2004 harvest seasons, 14 organic (certified by accredited organic agencies), 30 semi-organic (used organic practices but not certified) and 19 conventional farms were sampled to analyze 2029 pre-harvest produce samples (473 organic, 911 semi-organic, 645 conventional). Before each harvest season, a farmer survey was conducted to collect relevant information on farm management practices that might affect the risk of E. coli contamination in fresh produce. The use of animal wastes for fertilization of produce plants increased the risk of E. coli contamination in organic (OR=13.2, 95% CI=2.2-61.2, P-value<0.0001) and semi-organic (OR=12.9, 95% CI=2.9-56.3, P-value<0.0001) produce significantly. Improper ageing of untreated animal manure significantly increased this risk in organic produce (OR=4.2 95% CI=1.7-12.3, P-value=0.005) grown using such manure as a fertilizer. Organic growers who used cattle manure for fertilization of their crops showed significantly greater risk of contamination with the E. coli (OR=7.4, 95% CI=1.6-36.8, P-value=0.003), compared to those who used other types of manure-based fertilizer. In Minnesota, organic and semi-organic produce collected from the southeastern (SE) part of the state were at a significantly greater risk of E. coli contamination (OR=3.45, 95% CI=1.8-35.2, P=0.008), compared to those collected from farms located in the southern (S) regions of the state. In Wisconsin, organic and semi-organic produce collected from the southern (S) cluster of farms were at approximately 3-times greater risk of E. coli contamination (OR=2.67, 95% CI=1.3-9.4, P=0.004), compared to those grown in the northern (N) cluster of farms.