This article is aimed at discussing the structure of non-farm employment and small-scale non-agricultural enterprises in the rural areas where the rural-urban relation is increasing tremendously in the last decade. A special attention is devoted to the structure and sectoral as well as spatial linkages of small non farm enterprises (SNFE). In this context, rural-urban linkage is simply measured in terms of flow of materials, and labor from both rural to urban as well as from urban to rural areas. Interpretation of those flows is made to understand their respective implication for rural and regional development from which some policy recommendation are offered. An intensive single visit survey and rapid rural appraisal are conducted, covering three villages (Maguwoharjo, Kembang, Putat) in Yogyakarta Special Region (DIY). To some extent a qualitative information is also available for two additional villages of Pendowoharjo and Murtigading. This enables to draw a more complete picture of rural-urban linkage from and to all directions between Yogyakarta Municipality and its vicinity.