Chromosomes can be divided conceptually into autosomes and sex chromosomes.

An autosome is a chromosome that is not part of the organism's sex-chromosome system. A sex chromosome participates in a chromosomal system associated with sex determination or sex-specific inheritance patterns.

Humans provide one familiar example. Typical human females have two X chromosomes, while typical human males have one X and one Y chromosome:

$$XX\qquad\text{and}\qquad XY.$$

This is one biological system, not a universal rule for all organisms. Other species use different sex-determination systems.

X and Y are not fully homologous copies

The human X and Y chromosomes share small homologous regions but differ greatly over most of their lengths. Many loci present on the X chromosome do not have a corresponding allele-bearing locus on the Y chromosome.

For such an X-linked locus, an $XY$ individual carries only one allele copy rather than a homologous pair. This single-copy state is called hemizygosity.

If an X-linked locus has alleles $A$ and $a$, an $XX$ individual can have genotypes such as

$$X^AX^A,\qquad X^AX^a,\qquad X^aX^a,$$

whereas an $XY$ individual can carry

$$X^AY\qquad\text{or}\qquad X^aY.$$

For a locus absent from the corresponding region of Y, there is no second X-linked allele on the Y chromosome to mask or complement the X allele.

Sex-chromosome transmission is asymmetric

In the human XY system, an egg normally contributes an X chromosome. A sperm normally contributes either X or Y.

Therefore:

X egg + X sperm → XX zygote
X egg + Y sperm → XY zygote

An XY parent transmits its X chromosome to daughters in this simplified chromosomal model and its Y chromosome to sons; it does not transmit the same sex chromosome to both.

This transmission geometry is the basis for characteristic X-linked inheritance patterns.

The key conceptual distinction is that ordinary autosomal Mendelian reasoning assumes two homologous allele copies in a diploid individual, while a sex-chromosome system can create loci that are paired in one chromosomal sex but hemizygous in another.