Producers that graze or drylot cows in summer need to provide housing accommodations in winter. Cow comfort is an important consideration when selecting housing, particularly in areas with harsh winters. Alternative housing options being investigated in Minnesota include outwintering on a straw yard, and deep bedded compost. Stable flies, Stomoxys calcitrans (L.), are economically significant pests of dairy cows. Immature flies are found in decaying organic matter, such as soiled bedding. This research addressed how leftover debris from two winter housing systems, outdoor straw packs and indoor sawdust compost barns, differ in numbers and size of stable flies produced the following summer. Fly activity in summer are irritants that trigger defensive behaviors in cattle. Prolonged stress from flies can lead to significant production losses. This research also addressed the effect of three muscid fly species, stable flies, horn flies and face flies, on behavior and milk production of pastured cows.