We propose and demonstrate a method for measuring the spectral density matrix of a single photon pulse. The method is based on registering Hong-Ou-Mandel interference between a photon to be measured and a pair of attenuated and suitably delayed laser pulses described by a known spectral amplitude. The density matrix is retrieved from a two-dimensional interferogram of coincidence counts. The method has been implemented for a type-I down-conversion source, pumped by ultrashort laser pulses. The experimental results agree well with a theoretical model which takes into account the temporal as well as spatial effects in the source.