This paper analyzes the effects of different sources of R&D funding and patent office attributes on the patenting process. Another important contribution is modeling the effect of a random delay in the ‘pendency’ time as a stochastic process and quantifying its effect on patenting. The empirical estimation is based on four major industries – electronics, chemical and biology, transportation and aeronautics – for the time period 1976–1998. The primary results are: first, the source of R&D funding as well as performer (academic, federal and industry) has a differential effect on patenting. Second, the effects of some types of R&D and spillovers are different post-1990. Third, in the short run patenting is heavily influenced by patent office attributes. The state level analysis sheds light on the differing role of the federal government as an R&D performed and as a source of R&D funds for industry. The results contribute to a better understanding of the shortcomings in the formulation of science indicators.