A genotype describes the actual set (complement) of genes carried by an organism. In contrast, phenotype refers to the observable expression of characters and traits coded for by those genes.

Although phenotypes are based upon the content of the underlying genes comprising the genotype, the expression of those genes in observable traits (phenotypic expression) is also, to varying degrees, influenced by environmental factors.

The exact relationship between genotype and disease is an area of intense interest to geneticists and physicians and many scientific and clinical studies focus on the relationship between the effects of a genetic changes (e.g., changes caused by mutations) and disease processes. These attempts at genotype/phenotype correlations often require extensive and refined use of statistical analysis.

The term genotype was first used by Danish geneticist Wilhelm Johannsen (1857 – 1927) to describe the entire genetic or hereditary constitution of an organism, In contrast, Johannsen described displayed characters or traits (e.g., anatomical traits, biochemical traits, physiological traits, etc) as an organism's phenotype.

Genotype and phenotype represent very real differences between genetic composition and expressed form. The genotype is a group of genetic markers that describes the particular forms or variations of genes (alleles) carried by an individual. Accordingly, an individual's genotype includes all the alleles carried by that individual. An individual's genotype, because it includes all of the various alleles carried, determines the range of traits possible (e.g., a individual's potential to be afflicted with a particular disease). In contrast to the possibilities contained within the genotype, the phenotype reflects the manifest expression of those possibilities (potentialities). Phenotypic traits include obvious observable traits as height, weight, eye color, hair color, etc. The presence or absence of a disease, or symptoms related to a particular disease state, is also a phenotypic trait.

A clear example of the relationship between genotype and phenotype exists in cases where there are dominant and recessive alleles for a particular trait. Using an simplified monogenetic (one gene, one trait) example, a capital "T" might be used to represent a dominant allele at a particular locus coding for tallness in a particular plant, and the lowercase "t" used to represent the recessive allele coding for shorter plants. Using this notation, a diploid plant will possess one of three genotypes: TT, Tt, or tt (the variation tT is identical to Tt). Although there are three different genotypes, because of the laws governing dominance, the plants will be either tall or short (two phenotypes). Those plants with a TT or Tt genotype are observed to be tall (phenotypically tall). Only those plants that carry the tt genotype will be observed to be short (phenotypically short).