Indicative indexes and indicators of economic efficiency for the implementation of departmental target program "Sanitary protection of territory" in Irkutsk region were analyzed. The problem of the spread of the most dangerous infections and the concept of sanitary protection of the territory of Russian Federation were outlined. The result of the program was shown at the regional level. Indicator of cost efficiency for program adds information about results of the budget allocations' use. Required units give estimate the adequacy of the activity with respect to the result. Performance of the program's realization shows how efficiently resources were used. For the realization of program during the research period there is a slight decrease of effectiveness for budget expenditures due to imperfect mechanisms of results-oriented budgeting.