We report the novel synthesis of polymerase chain reaction (PCR)-derived single-stranded DNA (ssDNA) probes and their subsequent application in in situ hybridizations. Serial transverse sections of an 11.5-day postcoitum mouse embryo were hybridized to ({ }^{33} \mathrm{P}) SSDNA, ({ }^{33} \mathrm{P}-\mathrm{RNA}), or ({ }^{35} \mathrm{~S}-\mathrm{RNA}) probe corresponding to the same 181 -bp sequence in the myogenin cDNA. Signal obtained using ({ }^{33} P)-ssDNA was more intense than that using ({ }^{33} P)-RNA probe, while signal/noise ratios obtained with both ({ }^{33} \mathrm{P})-probes were far superior to those obtained with ({ }^{35} \mathrm{~S})-probe. Digoxigenin-labeled chicken growth hormone (GH) ssDNA gave slightly more intense signal than did digoxigenin-labeled chicken (G H) RNA when hybridized to chicken pituitary sections. ({ }^{32} \mathrm{P})-ssDNA probes were found to be suitable for Northern blot hybridization. Advantages of using ssDNA probes for in situ hybridization include: (1) The ssDNA technique is rapid and simple. There was no need to clone a DNA template into a special RNA vector or order special T7-containing PCR primers. ssDNA probes can be synthesized in less than 1 day using any primers which currently exist in a laboratory (optimal probe length for in situ hybridization is between 50 and 200 bp). (2) In three separate in situ experiments, sSDNA probes yielded more intense signal than RNA probes. (3) ssDNA probes are potentially more stable than RNA probes. (4) Since the RNAse rinse is eliminated, posthybridization rinses are shortened when hybridizing with ssDNA probes. The ssDNA probes produced by this protocol can be labeled with a variety of different isotopes (both radioactive and nonradioactive), and are excellent probes for use in in situ hybridizations. c 1993 Academic Press, Inc.