Polyatomic ions, often considered as causing interference in ICP-MS, SSMS and GDMS, are useful in thermal ionisation mass spectrometry (TIMS) for determining the atomic ratios of the elements, particularly for light elements. The objective of this paper is to provide a detailed discussion on the handling of the isotopic measurement data in TIMS using polyatomic ions, a useful technique for light elements, to reduce isotope fractionation effects. Taking as an example the Li2BO2+ ion for the determination of the Li-6/Li-7 or B-10/B-11 ratio of the unknown sample, a detailed theoretical analysis is presented for optimum selection of the pair of polyatomic ions to be used to determine the isotopic ratio of the element. The theory is supported by experimental data from the literature in three different examples: (i) the isotopic analysis of natural Li samples using the SRM-951-B isotopic standard; (ii) the isotopic analysis of an enriched Li-6 sample using SRM-951-B; (iii) the isotopic analysis of an enriched B-10 sample using natural Li (Svec standard). It is shown that the four polyatomic peaks observed in the m/z range of 54-57 are of practical importance. A qualitative idea can be obtained about the isotopic composition of Li and B in the sample (natural or enriched) based on the intensity distribution of these four peaks in the mass spectrum. When calculating accurate atomic ratios from the observed intensities of the polyatomic peaks, a simple ''rule of thumb'' should be kept in mind: the polyatomic ratio that is closer to the expected atomic ratio provides an accurate value of the atomic ratio of the element in the unknown sample. Even between the two polyatomic ion ratios, better accuracy is possible in cases which do not magnify the error during calculation and show less isotopic fractionation in the ion source. It has been stressed that the two peaks of highest intensity in the polyatomic ion are not necessarily the best for arriving at atomic ratios during the analyses of unknown samples, for depleted as well as enriched Li-6 and B-10 samples.