The aim of the paper is to study the implementation of the structural funds within Integrated Operational Programme of Regional Development (IOPRD), Priority 3 - Local Development, Measure 3.4. Micro-enterprises in Warmia and Mazury. As on December 31, 2005, the level of funds absorption from IOPRD 2004–2006 amounted to 81,0% and included 157 applications for investment subsidy. This reflects a high absorption of structural funds by entrepreneurs from Warmia and Mazury. The article also includes structural analysis containing such information as quantitative division of subsidies, periods of project realization, legal form of micro-entrepreneurs or type of business activity.