We report on an all-sky search for periodic gravitational waves in the frequency range 50−1000Hz with the first derivative of frequency in the range −8.9×10−10 Hz/s to zero in two years of data collected during LIGO's fifth science run. Our results employ a Hough transform technique, introducing a χ2 test and analysis of coincidences between the signal levels in years 1 and 2 of observations that offers a significant improvement in the product of strain sensitivity with compute cycles per data sample compared to previously published searches. Since our search yields no surviving candidates, we present results taking the form of frequency dependent, 95 confidence upper limits on the strain amplitude h0. The most stringent upper limit from year 1 is 1.0×10−24 in the 158.00−158.25Hz band. In year 2, the most stringent upper limit is 8.9×10−25 in the 146.50−146.75Hz band. This improved detection pipeline, which is computationally efficient by at least two orders of magnitude better than our flagship Einstein@Home search, will be important for "quick-look" searches in the Advanced LIGO and Virgo detector era.