To optimize control of an avian influenza outbreak knowledge of within-flock transmission is needed. This study used field data to estimate the transmission rate parameter (β) and the influence of risk factors on within-flock transmission of highly pathogenic avian influenza (HPAI) H7N7 virus in the 2003 epidemic in The Netherlands. The estimation is based on back-calculation of daily mortality data to fit a susceptible-infectious-dead format, and these data were analysed with a generalized linear model. This back-calculation method took into account the uncertainty of the length of the latent period, the survival of an infection by some birds and the influence of farm characteristics. After analysing the fit of the different databases created by back-calculation, it could be concluded that an absence of the latency period provided the best fit. The transmission rate parameter (β) from these field data was estimated at 4.50 per infectious chicken per day (95% CI: 2.68–7.57), which was lower than what was reported from experimental data. In contrast to general belief, none of the studied risk factors (housing system, flock size, species, age of the birds in weeks and date of depopulation) had significant influence on the estimated β.