Ah yes, Japanese, the language of great culture, deep meaning and infectiously cute cartoons. Like much like our language, english, Japanese has a few (a lot) of words that sound the same, but have different meanings, and are also somtimes not spelled the same, they are homophones. Here are a few examples (this has been extended to include pharases. Keep in mind that the kanji are all different, and some may be imported words in most cases):

Hana - flower
Hana - nose
Seishi wo kakeru - to stake one's life
Seishi wo kakeru - to spray sperm on somthing
Chizu - map
Chiizu - cheeze

Cases where confusion can arise:

1. One day mom buys new flowers, and places them in a vase near the dining table. During dinner, her son says to her "Hana ga kirei dane"(the flowers are pretty), and she mistakenly became very happy about her son.

2. Grandmother says "takusan kumo ga detekita" (lots of clouds are coming out) to which her grandson paranoidly responds "where? when?"

3. Stranger calls house, little kid picks up. Stranger says "okaasan iru?" (Is your mom there?) The child responds: "iranai!" (no thank you!)

Some homophones:

dekiru - has skill (ex: "kare wa dekiru" = "he's got skill")
dekiru - to be able to
dekiru - to conceive a life form
furu - to fall, pour ("ame ga furu" == "rain falling")
furu - to shake
haku - throw up
haku - to put on (ex: "kutsu wo haku" = "to put on shoes")
hana - flower
hana - nose
iru - at/exist
iru - need/want
kaburu - to get a rash
kaburu - to wear (ex: "booshi wo kaburu" = "to wear a hat")
kaki* - mussel
kaki* - persimmon
kaku - to itch
kaku - to write
kiku - chrysanthemum
kiku - to be effective
kiku - to listen to
kiru - to cut
kiru - to wear (ex: "T-shatsu wo kiru" = "to wear a T-shirt")
kumo - cloud
kumo - spider
sake - rice wine
sake - salmon fish (syn: shahke)
tatsu* - dragon
tatsu* - to stand
umi - ocean, sea
umi - oozing puss

re Broccolist: True, chizu and chiizu are not homophones, and the difference should be discernable to a speaker of almost any language upon hearing. There are pseudo-homophones that have tone difference(Japanese accent), as you point out. The fake ones are marked with asterisks.
Yes, Japanese has loads of homophones. But most of them have completely different meanings, so there's no risk of confusing them. It doesn't really make learning Japanese any harder.

Many of those aren't really homophones, anyway. In "chiizu" (cheese), the 'i' is doubled, whereas in "chizu" (map), it isn't. This is a huge difference to Japanese ears, cheese is 1 beat longer: it's impossible to mix them up. As for "hana" (nose) and "hana" (flower), one of them has an accent on the 'na' (not written, only in speech) in standard Japanese, which causes words following it to have a lower pitch. "iru" (to be) and "iru" (need) aren't the same type of verb, so in almost every form, they won't be pronounced the same.

See? Japanese isn't so bad. If you think Japanese is complicated, try English.

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