The process of country’s modernization as well the socio-economic development and improvement of living conditions of the population bears the purpose to coordinate, stimulate and implement the mechanisms of innovation activities in Moldova. Currently innovation activity is regulating and assisting as on the state level – by the Academy of Sciences, the Agency for innovation and technology transfer (AITT), the State Agency on intellectual property (AGEPI), and on the non-governmental level – by various organizations, such as Small business Association (SBA) etc. In the framework of SBA activity was implemented the investigation of the basic sectors of Moldovan SMEs innovation projects and main problems in this field. The AITT’s data and personal interviews with entrepreneurs were used for this investigation. Consequently, the priority sectors of Moldovan SME’s innovation projects were defined, such as: agricultural technologies and food industry technologies. As well the main problems in SME’s innovation activity are: insufficient competence, financial provision etc.