A computer program (the program, TNC3, is written in FORTRAN 77 and is designed to run on a microcomputer. A copy of this program on a 5.25 inch disc may be obtained from Dr R. Martin, Peter MacCallum Cancer Institute, 481 Little Lonsdale Street, Melbourne, Victoria 3000, Australia. FAX number 61-3-670-3357) is described which calculates average dose and dose distributions in cell nuclei from ions produced by thermal neutron nuclear reactions in nitrogen and 10B. The program allows different concentrations of nitrogen and boron in the cell nucleus, its cytoplasm and outside the cell to be treated. The case of boron carried by antibodies is also dealt with. The cell and its nucleus are modelled as ellipsoids, which allows a range of cell and nuclear shapes to be treated. This analysis reveals the importance of the distributions of the target atoms on a microscopic scale. In particular, for nitrogen atoms, the assumption that the concentration in the nucleus is the same as in the cytoplasm may lead to significant errors in determining average dose. Detailed examples of dose calculations are given to illustrate the type of analysis that is possible using the program. Microdosimetric spectra of doses to the nucleus are also described for a case of constant average dose for various concentrations of uniformly distributed boron. The dose is held constant by varying the neutron fluence. Here it is shown that the spectrum does not change, suggesting that the biological effect is independent of the uniform boron concentration as long as the dose is held constant.