The impact of agglomeration on the quantitative assessment of thermal spore inactivation was investigated. The agglomeration size distribution in suspensions of Bacillus stearothermophilus spores was determined by using a three-fold dynamic optical back-reflexion measurement (3D ORM). Thermal inactivation data have been modelled using first-order inactivation kinetics, superimposed by the agglomeration size. Since 3D ORM accurately yields the maximum length of an agglomerate, but provides no information on the packing density, two limiting cases have been discriminated in mathematical modelling: three-dimensional, spherical packing for maximum spore count and two dimensional, circular packing for minimum spore count of a particular agglomerate. Thermal inactivation studies have been carried out in thin glass capillaries where by using numerical simulations the non-isothermal conditions were modelled and taken into account. It is shown that the lag phase often found in thermal, spore inactivation (shoulder formation) can sufficiently be described by first-order inactivation. kinetics when the. agglomeration size is considered. (c) 2006 Elsevier Ltd. All rights reserved.