The historical origins and the movements of human populations have intrinsic, mainly cultural value, but bear also on the genetic epidemiology. Small populations, such as that of Malta (2006 ~ 400,000) in the process acquire genetic structure. It may vary rapidly over time due to rates of population growth, admixture, and age distribution based on socio-economic development. The spectrum of mutations and polymorphisms that ensues may contribute to gene discovery, in-vivo expression profiling, with genetics therapeutics and public health policy outcomes.

We shall describe the demographics and Y chromosome haplotypes of the contemporary Maltese population following a millennium of growth characterised by two alternate genetic models and early admixture from neighbours and later from distant populations respectively. Using qRFLP with pools of mixed DNA from selected collections we refer to frequencies of critical alleles in Globin, G6PD, CFTR, Haemostasis and some other loci which could be influenced by founder effects or drift resulting in genetic homogeneity or others which are heterogeneous. The data equally bear on the organisation of Maternal & Neonatal Testing Programmes. Based on a haemoglobin paradigm of complex disease due to multiple genes with quantitative effects, we shall argue that, on the basis of a common disease due to a few common variants, it can be shown that, interplay between two alleles at two loci could generate quantitative biochemical heterogeneity over a whole range from under 10% to around 100% of a particular polymorphic molecule.