Quantitative scanning transmission electron microscopy (STEM), implemented on a conventional transmission electron microscope with STEM-attachment, has been a primary tool in our laboratory for the quantitative analysis of collagen fibril assembly in vivo and in vitro. Using this technique, a precise measurement of mass per unit length can be made at regular intervals along a fibril to generate an axial mass distribution (AMD). This in turn allows the number of collagen molecules to be calculated for every transverse section of the fibril along its entire length. All fibrils show a near-linear AMD in their tip regions. Only fibrils formed in tissue environments, however, show a characteristic abrupt change in mass slope along their tips. It appears that this tip growth characteristic is common to fibrils from evolutionarily diverse systems including vertebrate tendon and the mutable tissues of the echinoderms. Computer models of collagen fibril assembly have now been developed based on interpretation of the STEM data. Two alternative models have so far been generated for fibril growth by accretion; one is based on diffusion limited aggregation (DLA) and the other based on an interface-limited growth mechanism. Inter-fibrillar fusion can also contribute to the growth of fibrils in vertebrate tissues and STEM data indicates the presence of a tight regulation in this process. These models are fundamental for the hypotheses regarding how cells synthesise and spatially organise an extracellular matrix (ECM), rich in collagen fibrils.