Abstract Background Giardia duodenalis is a ubiquitous protozoan parasite that has emerged as a significant opportunistic human pathogen. G. duodenalis may have a deleterious effect on animal growth and performance, therefore its potential as a production limiting organism should not be discounted. We therefore undertook this study to determine management and environmental factors in feedlots that influence the prevalence and environmental load of G. duodenalis cysts in fecal material deposited by feedlot cattle in the central and western United States. Results Twenty two feedlots from 7 states were included in the study, and up to 240 fecal samples were collected from pen floors of up to 6 pens per feedlot. Giardia duodenalis cysts were identified and counted using direct immunofluorescent microscopy. The estimated overall point prevalence of G. duodenalis was 19.1%, representing feedlots from a wide range of climates and management systems. Pen-level prevalence varied from 0 to 63.3%, with pen-level shedding estimates ranging from 0 to 261,000 cysts/g feces. Higher environmental temperatures, increased animal density, and increased time in the feedlot were associated with a lower prevalence of G. duodenalis. Removing manure before placing a new group of cattle in a pen was associated with a decreased prevalence of G. duodenalis in fecal pats. Using coccidiostats as a feed additive was associated with a higher prevalence of Giardia. Conclusion Management practices could be employed that would limit the probability that feedlot cattle shed G. duodenalis in their feces and therefore potentially limit contamination of their environment.