Pectins are a major component of plant cell walls and have numerous roles in plant growth and development. Extracted pectins are widely used as functional food ingredients in products including ice creams, jams, jellies and milk drinks. Although all are based on a galacturonan-rich backbone, pectins are an immensely diverse family of polysaccharides, the functional properties of which are dictated by their fine structures. Understanding the biological roles of pectins and optimizing their industrial usage requires a detailed knowledge of their diversity and spatial and temporal distributions, and microarray technology is a promising tool for high throughput pectin analysis. This article discusses the technical aspects of the production of pectin microarrays and explores their current and potential future uses in the context of recent work in the field.