This paper is dedicated to the research topical and practical aspects of problems of risks estimation in the enterprise of pharmaceutical manufacturing. Risks of products’/markets’ concentration and ecological risks are the most essential for the company at present – that is clarified in the research. The autors propose usage of model of ERM to manage risks of the pharmaceutical company. Such parameters of risks are evaluated in the article: company’s value by using conception of EVA; risks of company’s stock (share) by using statistical, beta coeficient and VaR historical modeling methods; risks of products’/markets’ concentration and ecological risks by using method of scenarios and method of sensitive analysis. Efficiency of realization of the ecological project are estimated in the research both qualitatively (assessment of experts) and quantitatively (the project influence to EVA). Proposals are drafted by the authors for risks management of the enterprise.