The future of human embryonic stem cell (hESC) research with regards to their applicability in a therapeutic setting, relies on the development and standardisation of consistent and robust methods to demonstrate their defining characteristics; their pluripotent ability to form all three germ layers and their capacity for self-renewal. Although much research has been carried out to investigate new methods of culturing hESCs, many of these studies have not robustly concluded the impact of prolonged culture on genetic and genomic stability nor have they examined in any comparative detail the impact of the culture conditions such as differences in feeders used or the media composition in which the stem cells are cultured in. The aim of this thesis therefore was to investigate and evaluate methods for improving the uniform and robust culture and characterisation of hESCs over prolonged periods in culture. Four hESC lines ( RH5, HUES9, SHEF1 and NCL5) were chosen on the basis that they had not previously been well characterised and therefore could potentially benefit the wider stem cell community by increasing diversity, rather than continue to use the already small subset of well publicised lines. The RH5, HUES9, SHEF1 and NCL5 cells were subjected to long term passaging using recombinant enzyme TrypLEâ„¢ Express, on human feeders, mouse feeders and feeder free matrix Matrigel in combination with defined media mTeSR1, for uniform scale up. Changes in characteristic stem cell surface markers were compared using two techniques; flow cytometry and quantitative in situ fluorescence microscopy. Genomic stability was assessed by real time PCR. Chromosomal integrity was monitored using array genomic hybridisation (aCGH). Array genomic hybridisation analysis of cells cultured for 20 passages by enzymatic passaging revealed changes in copy number variations in all the stem cell lines. Aberrations on chromosomes 12, 17 and 20, appeared most commonly as a result of long term culture. Although no significant differences were seen between hESCs cultured on mouse and human feeders, cultures on Matrigel showed fewer detected chromosomal aberrations. Expression of cell surface stemness markers SSEA3, SSEA4, TRA1-60 and TRA1-81 were maintained by hESC cultured on all matrices and confirmed by the use of flow cytometry and high throughput quantitative immunofluorescence imaging using the TissueFaxsâ„¢ cell analysis microscopy system. In depth imaging revealed subtle but important differences in the way in which hESCs attach and proliferate on different matrices. Genetic profiling of each of the stem cell lines using Taqman Low density array cards to assess the expression of 96 genes by Real Time PCR, demonstrated the continued expression of stemness genes 21 at late passage, and low level expression of differentiation genes, inherent to particular stem cell lines. Although both mouse and human feeders and Matrigel support the undifferentiated growth of hESCs, subtle differences from the hESCs were seen as a result of their use, most obviously, changes in morphology and how they proliferate. This was further explored in the stem cell line NCL5, as it demonstrated a readiness to adapt to new matrices, better chromosomal stability and higher expression of cell surface markers compared with the other hESC lines. Using in vitro differentiation assays to all three germ layers, NCL5 cultured to late passage (p+20) on human feeder iMRC5, mouse feeder iMEF and feeder free matrix Matrigel, demonstrated the ability to differentiate to ectoderm, endoderm and mesoderm progenitors after induction using three 7 day flat based directed differentiation protocols. Altered differentiation patterns were detected by Real Time PCR and TissueFaxsâ„¢ imaging and quantitative analysis, as a consequence of the prolonged culture on the specific matrices used. Such key findings allude to the strong influences of microenvironment and will help to improve the standardisation of in vitro differentiation assays. From these studies, chromosomal changes had no impact on NCL5 stem cell linesâ€˜ ability to form progenitors, however small genetic instabilities may still play a role in terminal differentiation of germ lineage specific cell types. The findings of the programme of work described has led to the successful culture methods and characterisation testing validated in this project being incorporated into routine culture and banking of research grade hESCs at the UK Stem Cell Bank. These protocols will now be made more widely available and should assist stem cell researchers in adopting the most suitable and optimum conditions for culturing stem cells in the undifferentiated and stable state. With the huge surge in stem cell research over the past decade, the development of robust characterisation and culture methods will undoubtedly have significant impact on the exploitation of these cells for regenerative medicine and to assist with this a future aim of the stem cell bank will be to standardise methodologies for clinical grade banking.